##################################################################################
#
# EMIL module for calculation of absolute free energies of biomolecules.
# By Joshua T Berryman, University of Luxembourg, 2013.
#
# This code is covered by the GPL, except when distributed with non-gpl parts of
# AMBER (when it is covered by the same licence as the rest of that distribution).
# See licence.txt in the source directory.
#
# If you use this module for research, please cite:
#                         Joshua T Berryman and Tanja Schilling,
#                         J. Chem. Theory Comput., 2013, 9 (1), 679-686.
#
#
##################################################################################
# Setting up emil, with boxinfo: 72.985 73.5808 74.6288
# read parameters:
# N 1341
# seed 1992 Displ 0.2
#
# Setting well types
# marking 919 of 1341 atoms as heavy
# matching 435 atoms as chain roots
# mask DC,DG,DA,DT,DA5,DT5,DA3,DT3,DG5,DG3,DC5,DC3 sets type of 754 atom wells as 1 of 7
# mask Na+ sets type of 189 atom wells as 4 of 7
#    ...created liquid with exchange-symmetry between 189 chains.
# mask Cl- sets type of 167 atom wells as 4 of 7
#    ...created liquid with exchange-symmetry between 167 chains.
# mask WAT sets type of 231 atom wells as 4 of 7
#    ...created liquid with exchange-symmetry between 77 chains.
#
# Initialising wells
# Well type Einstein Molecule has parameters:
#   r s.t. E=0: 1
#   epsilon:    5
#   A/well:    -4.30294
#
# Well type Wingwell Liquid   has parameters:
#   k1:         1.112
#   r1:         1
#   wing force: 1.111
#   r2:         5
#   depth:      5
#   A/well:    -12.8998
#
# Well type Relative position has parameters:
#   r s.t. E=0: 1
#   epsilon:    5
#   A/well:    -4.30294
#
#
# Reading well positions from wellsIn.dat
# msd part-well is: 3398.33
# Finished setting particle well types:
# Null              0
# Einstein Molecule 754
# Conewell Liquid   0
# Harmonic Liquid   0
# Wingwell Liquid   433
# Wobblium          0
# Relative position 154
# 1187 heavy or solute atoms.
# Building well neighbour list. 
# Linking particles to wells. 
# Linked particles to wells, rms distance (heavies): 5.33032e-15
# N heavies or roots: 1187
# Molecule-Well assignment for indistinguishable fluid: 1 will be updated using:
# Monte Carlo      
# Molecule-Well assignment for indistinguishable fluid: 2 will be updated using:
# Monte Carlo      
# Molecule-Well assignment for indistinguishable fluid: 3 will be updated using:
# Monte Carlo      
# done setup.
#
# Energy units: initial beta  1.67741 == 1.0 / 0.596158
# Scaling forces using polynomial mixing functions, at lambda = 0.9 :
# scaling amber forces by 0
# scaling soft force by   3.69056e-05
# scaling EMIL forces by  0.81
# Uncorrected EABS is: -6705
# With offset of 0 this is: -6705
#
# Reporting EMIL abstract Helmholtz free energy,
# according to equations in supp. data of Berryman & Schilling, JCTC 2013: 
# liquid 1 has nchains: 189 and log(N!): 8.052304e+02
# liquid 2 has nchains: 167 and log(N!): 6.911834e+02
# liquid 3 has nchains: 77 and log(N!): 2.605649e+02
# Total free energy A of abstract model (units kT): -7.735712e+03
# A-Solid: -3.244415e+03 A-Liquid: -6.248275e+03 A-degen: 1.756979e+03
#
# Total free energy A of abstract model (units of calling program): -4.611703e+03
# A-Solid: -1.934182e+03 A-Liquid: -3.724956e+03 A-degen: 1.047436e+03
#
#
# Generalised forces will be reported in units of calling program, not in kT/A
#
# emil mol_lambda: 0.9 abstract_lambda: 0.9
#
# (mixed)  ABS_ENTH(kT) -5431.05 MOL_ENTH 0 TOT      -5431.05
# (native) ABS_ENTH(kT) -6705 MOL_ENTH 0 TOT      -6705
#
Reloc acceptance rate: 0 Swap acceptance rate: 0.0232558
nstep:  0 soft_dHdL:  -6.17018505e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -7.18429409e+03
Reloc acceptance rate: 0 Swap acceptance rate: 0.0116279
nstep:  1 soft_dHdL:  -6.17143947e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -7.18233637e+03
Reloc acceptance rate: 0 Swap acceptance rate: 0.0155039
nstep:  2 soft_dHdL:  -6.17295620e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -7.16574773e+03
Reloc acceptance rate: 0.00581395 Swap acceptance rate: 0.0290698
nstep:  3 soft_dHdL:  -6.17468180e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -7.11848739e+03
Reloc acceptance rate: 0.0139535 Swap acceptance rate: 0.0511628
nstep:  4 soft_dHdL:  -6.17611769e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -7.08355033e+03
Reloc acceptance rate: 0.0232558 Swap acceptance rate: 0.0697674
nstep:  5 soft_dHdL:  -6.18234192e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -7.00739888e+03
Reloc acceptance rate: 0.0299003 Swap acceptance rate: 0.0797342
nstep:  6 soft_dHdL:  -6.21359561e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -6.97600952e+03
Reloc acceptance rate: 0.0261628 Swap acceptance rate: 0.0843023
nstep:  7 soft_dHdL:  -6.21614509e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -6.90908968e+03
Reloc acceptance rate: 0.0258398 Swap acceptance rate: 0.0904393
nstep:  8 soft_dHdL:  -6.21820273e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -6.85505901e+03
Reloc acceptance rate: 0.0255814 Swap acceptance rate: 0.1
nstep:  9 soft_dHdL:  -6.22040877e+02 molec_dHdL:  0.00000000e+00 abstr_dHdL:  -6.84092462e+03